Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Bray, Marcus S; Wu, Jianmin; Padilla, Cory C.; Stewart, Frank J.; Fowle, David A.; Henny, Cynthia; Simister, Rachel L.; Thompson, Katherine Jenny; Crowe, Sean A.; Glass, Jennifer B.

doi:10.1111/1758-2229.12809

Cited by 19 publications

(16 citation statements)

References 62 publications

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“…Given our main objective of identifying potentially electroactive bacteria, we analyzed genomes containing many (or very large) multiheme c -type cytochromes (MHCs), which are fundamental in most known EET pathways ( Shi et al, 2009 , 2016 ; Wrighton et al, 2011 ). We also searched genomes for putative type-IV “e-pili” known to be involved in EET in Geobacter and likely in other taxa ( Walker et al, 2018 , 2020 ; Bray et al, 2020 ). Table 1 includes the 31 genomes found to have such genes.…”

Section: Resultsmentioning

confidence: 99%

“…Potential e-pili were identified largely following the methods of Bray et al (2020). The model and query protein sequence was PilA from Geobacter metallireducens GS-15 (WP_004511668.1, locus Gmet_1399) (Tan et al, 2017).…”

Section: Identification Of Protein-coding Genes Implicated In Extracementioning

confidence: 99%

“…All resulting sequences (n = 272) were analyzed using Pilfind 9 to help verify pili sequences as type-IV (Imam et al, 2011), leaving 224 sequences. A Python script made freely available 10 by Bray et al (2020) was used to calculate the number of aromatic amino acids (F, W, Y, and H), the length of the mature pilin sequence, and the percentage of aromatic residues. Sequences with ≥8% aromatic residues were then manually selected by building MAFFT (v7.309) protein alignments (Katoh and Standley, 2013) in Geneious (v9.1, Biomatters) and inspection of aromatic spacing and distribution.…”

Section: Identification Of Protein-coding Genes Implicated In Extracementioning

confidence: 99%

“…in other taxa (Walker et al, 2018(Walker et al, , 2020Bray et al, 2020). Table 1 includes the 31 genomes found to have such genes.…”

Section: Genomes Rich In Multiheme Cytochromes And/or Putative E-pilimentioning

confidence: 99%

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Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities

2020

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Extracellular electron transfer (EET) between microbes and iron minerals, and syntrophically between species, is a widespread process affecting biogeochemical cycles and microbial ecology. The distribution of this capacity among microbial taxa, and the thermodynamic controls on EET in complex microbial communities, are not fully known. Microbial electrochemical cells (MXCs), in which electrodes serve as the electron acceptor or donor, provide a powerful approach to enrich for organisms capable of EET and to study their metabolism. We used MXCs coupled with genomeresolved metagenomics to investigate the capacity for EET in microorganisms present in a well-studied aquifer near Rifle, CO. Electroactive biofilms were established and maintained for almost 4 years on anodes poised mostly at −0.2 to −0.25 V vs. SHE, a range that mimics the redox potential of iron-oxide minerals, using acetate as the sole carbon source. Here we report the metagenomic characterization of anode-biofilm and planktonic microbial communities from samples collected at timepoints across the study period. From two biofilm and 26 planktonic samples we reconstructed draftquality and near-complete genomes for 84 bacteria and 2 archaea that represent the majority of organisms present. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes (MHCs) was the dominant electrode-attached organism. However, a diverse range of other electrode-associated organisms also harbored putative MHCs with at least 10 heme-binding motifs, as well as porin-cytochrome complexes and e-pili, including Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Betaand Gammaproteobacteria. Our results identify a small subset of the thousands of organisms previously detected in the Rifle aquifer that may have the potential to mediate mineral redox transformations.

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Section: Resultsmentioning

confidence: 99%

Section: Identification Of Protein-coding Genes Implicated In Extracementioning

confidence: 99%

Section: Identification Of Protein-coding Genes Implicated In Extracementioning

confidence: 99%

“…in other taxa (Walker et al, 2018(Walker et al, , 2020Bray et al, 2020). Table 1 includes the 31 genomes found to have such genes.…”

Section: Genomes Rich In Multiheme Cytochromes And/or Putative E-pilimentioning

confidence: 99%

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Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities

2020

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“…Following the publication of the article by Bray et al . (), the authors alerted the Journal to the fact that, in Figure , the boxes for amino acids 24, 27, 32, 50, 51, and 57 are incorrectly aligned. The amended Figure is shown below.…”

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confidence: 99%

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

2020

Environ Microbiol Rep

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Conductive proteins‐based extracellular electron transfer of electroactive microorganisms

Zhang,

You,

Liu

et al. 2023

Quant. Biol.

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Electroactive microorganisms (EAMs) could utilize extracellular electron transfer (EET) pathways to exchange electrons and energy with their external surroundings. Conductive cytochrome proteins and nanowires play crucial roles in controlling electron transfer rate from cytosol to extracellular electrode. Many previous studies elucidated how the c‐type cytochrome proteins and conductive nanowires are synthesized, assembled, and engineered to manipulate the EET rate, and quantified the kinetic processes of electron generation and EET. Here, we firstly overview the electron transfer pathways of EAMs and quantify the kinetic parameters that dictating intracellular electron production and EET. Secondly, we systematically review the structure, conductivity mechanisms, and engineering strategies to manipulate conductive cytochromes and nanowire in EAMs. Lastly, we outlook potential directions for future research in cytochromes and conductive nanowires for enhanced electron transfer. This article reviews the quantitative kinetics of intracellular electron production and EET, and the contribution of engineered c‐type cytochromes and conductive nanowire in enhancing the EET rate, which lay the foundation for enhancing electron transfer capacity of EAMs.

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Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Cited by 19 publications

References 62 publications

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Conductive proteins‐based extracellular electron transfer of electroactive microorganisms

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